Up to date WSJT-X .deb and .rpm files are available directly from Joe Taylor for WSJT-X, which includes WSPR. Be sure you get the amd64 variant in general.
.deb WSJT-X file by
sudo gdebi wsjtx*.deb
The WSJT-X program is very robust and reliable. It decodes multiple streams at once, JT9 and JT65, even overlapping signals!
Setting JT9/JT65 divider frequency
I set 2600 Hz as the divider between JT65 (below 2600 Hz) and JT9 (above 2600 Hz). Some people use +/- 100 Hz from this.
JT65/JT9 transmit power
Control your output power with your sound card output level, NOT with your radio’s RF power control. If you have your radio transmitter slamming hard into ALC (by maxing audio output and turning RF power control down) you will be splattering (interfering with adjacent frequencies), just like other digital modes in general. Most people use 1 to 25 Watts transmit power for JT65 and JT9.
JT65 and JT9 on 60 meters
For 60 meters, remember that 2.8 kHz is the upper edge of the channel for USA users.
Using WSJT-X on older radio with 2.4 kHz filtering
While these too-narrow filters do not have infinitely steep skirts, you will certain take an SNR penalty outside their bounds. I notice that most stations operate at no less than 300-400 Hz above carrier frequency, so by using your IF shift (or PBT), you can cover from 400-2800 Hz, with ability to hear stronger 3000 Hz JT9 stations. It’s a tradeoff between missing stations on the edge of either band. I notice that JT65 DX sometimes does down as low as 300 Hz (typically accomplished by their radio using Split TX frequency). I have also see JT9 as high as 3500 Hz and beyond.
Optimal solution: SDR for receive
If you are interested in contributing to ionospheric science, you need a radio that receives on multiple bands, multiple modes simultaneously. That is capturing CW, JT65, JT9, WSPR, etc. simultaneously. You can do single-band, multimode reception with a FlexRadio 1500, RFSpace SDR-IQ, et al. Simultaneous multi-band reception can be accomplished with a bank of SoftRock receivers or a QS1R, and so on. Another cost-effective and powerful way is to do it yourself with an instrument like Red Pitaya, but you might start with a commercial SDR receiver and go from there.